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1 # Copyright 2006 by Peter Cock. All rights reserved. 2 # 3 # This code is part of the Biopython distribution and governed by its 4 # license. Please see the LICENSE file that should have been included 5 # as part of this package. 6 """Bio.SeqIO support for the "nexus" file format. 7 8 You were expected to use this module via the Bio.SeqIO functions. 9 This module has now been replaced by Bio.AlignIO.NexusIO, and is 10 deprecated.""" 11 12 import warnings 13 warnings.warn("Bio.SeqIO.NexusIO is deprecated. You can continue to read" \ 14 + " 'nexus' files with Bio.SeqIO, but this is now" \ 15 + " handled via Bio.AlignIO internally.", 16 DeprecationWarning) 17 18 from Bio.Seq import Seq 19 from Bio.SeqRecord import SeqRecord 20 from Bio.Nexus import Nexus 21 22 #You can get a couple of example files here: 23 #http://www.molecularevolution.org/resources/fileformats/ 24 25 #This is a generator function!27 """Returns SeqRecord objects from a Nexus file. 28 29 Thus uses the Bio.Nexus module to do the hard work.""" 30 n = Nexus.Nexus(handle) 31 for id in n.original_taxon_order : 32 if id in n.matrix : 33 seq = n.matrix[id] 34 else : 35 #Missing the sequence? 36 seq = Seq("", n.alphabet) 37 #ToDo - Can we extract any annotation too? 38 yield SeqRecord(seq, id=id, name=id, description="") 39 #All done 40 return41
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